[Objective] Taking the Chezhegou basin in the intensively agricultural Huaibei Plain as a case study, this research scientifically evaluates the water ecological health from the perspective of ecosystem integrity, considering the unique watershed characteristics of agricultural intensive areas. This study aims to provide practical technical support for the ecological restoration of lake-like rivers in similar regions, and offer a scientific basis for regional water ecological security and sustainable management. [Methods] An evaluation framework for aquatic ecology in agricultural-intensive area was constructed in consideration of water resources, water environment, and water ecology (WRE). Seven key indicators were selected using principal component analysis (PCA, cumulative variance explanation rate >97%) and entropy weight method, considering data accessibility, indicator frequency (≥0.05), and alignment with national standards. The final indicators included: water resource utilization rate, water exchange cycle, comprehensive trophic level index, phytoplankton diversity index, aquatic plant coverage, phytoplankton density, and natural riparian ratio. Statistical analyses (ANOVA, correlation analysis) were also performed. [Results] (1) The Chezhegou basin exhibited distinct lake-type river features: water exchange cycles ranged from 110 to 179 days (mean 119 days) due to low slope (0.2‰), dam interception, and tributary backwater, forming a “semi-stagnant water” state. Water resource utilization rate averaged 43%, reflecting high reliance on agricultural irrigation. Water level (mean 26.40 m) was positively correlated with rainfall (r=0.78, p<0.01) but showed significant lag effects (4-28 hours, mean 12.6 hours) and asynchronous responses to rainfall intensity, attributed to artificial dam regulation. (2) Physicochemical parameters showed significant spatiotemporal variability: TN (0.40-9.51 mg/L, mean 2.52 mg/L), TP (0.002-1.46 mg/L, mean 0.137 mg/L), COD_Mn (1.2-17.8 mg/L, mean 4.86 mg/L), and Chl-a (10.7-23.4 μg/L, mean 18.3 μg/L) fluctuated seasonally, with higher values in the wet season (except TN). Spatially, Chl-a, TP, and COD_Mn were significantly higher in the midstream than upstream and downstream. The TLI ranged from 50 to 60 (mild eutrophication), with midstream points reaching moderate eutrophication (TLI=62.3-65.1) in June-July 2023. (3) Eight aquatic plant species were identified, with emergent plants (e.g., Phragmites australis) accounting for 50%. Phytoplankton included 7 phyla and 71 species, dominated by Chlorophyta (46.48%) and Bacillariophyta (22.54%). Phytoplankton density averaged 721.45×10⁴ ind./L, and the Shannon index ranged from 1.86 to 2.213 (mean 1.92), indicating low biodiversity. Chlorophyta abundance was positively correlated with TN (r=0.68, p<0.01) and TP (r=0.72, p<0.01), reflecting eutrophication-driven community succession. (4) The health assessment results showed that the overall water ecological health score averaged 58.22, classified as Grade III (Moderate). Seasonally, summer scores (mean 54.42) were significantly lower than spring (60.72), autumn (59.51), and winter (59.01) (p<0.05), driven by higher summer TLI (mean 62.3) and lower phytoplankton diversity. Interannually, scores declined from 58.38 (2022) to 56.17 (2023) and recovered to 60.10 (2024), consistent with eutrophication dynamics. [Conclusions] The results confirm that the Chezhegou basin’s moderate health status is primarily constrained by eutrophication and low biodiversity. The assessment system, with a cumulative variance explanation rate of 97.202%, demonstrates highly scientific rigor and practicality, offering a replicable tool for similar ecosystems. Future research should enhance monitoring of zooplankton and benthic invertebrates to improve food chain representation.